(CNN)Bryan Pagliano, the former State Department IT specialist who managed Hillary Clinton's private email server, was hired by the State Department as a political appointee -- an unusual arrangement within his department that caused confusion among some managers.

A new set of emails from early 2009, which were released to the conservative legal watchdog group Judicial Watch as part of an ongoing Freedom of Information Act lawsuit, reveals conversations between top State Department officials about how the Bureau of Information Resource Management (IRM) could go about hiring Pagliano as an IT specialist under this arrangement.

Pagliano had previously worked as an IT director for Clinton's 2008 presidential campaign.

The emails show that Pagliano's resume was initially sent to Patrick Kennedy, the under secretary for management, in mid-February 2009. Kennedy passed the resume to Susan Swart, the chief information officer at IRM, and Charles Wisecarver, the deputy chief information officer for operations.

Wisecarver apparently met with Pagliano in early March, at which point he sought guidance on bringing in a political appointee -- also referred to as a "Schedule C" employee.

Read More

"Pat (Kennedy) passed on resume of a young man who ran technology for the Clinton for President campaign," Wisecarver wrote on March 9. "Janice and I met with him on Friday and see the value in bringing him on. (Redaction) What now? IRM doesn't have a lot of experience with 'schedule c' types."

A couple days later, a human resources manager writes to explain that Pagliano will need to officially report to Kennedy because "Schedule C" employees must report to Senate-confirmed officials within the department.

"As a Schedule C, Bryan must report to a PAS (Presidential Appointee with Senate confirmation)," the manager writes, "and since Ms. Swart is not a PAS, the (position description) should identify U/S Kennedy as the supervisor."

Still, in a separate email conversation between Wisecarver and Swart during the same timeframe, the two appear to question the arrangement.

"Your (sic) not a PAS! What is a PAS? Is this a reference for a confirmed (Assistant Secretary)?" Wisecarver asks.

"I don't know what a pas is," Swart replies. "(Patrick Kennedy) specifically said we didn't need to be pol apptees but it sure sounds like we do."

Swart ends the email with the incomplete sentence: "What a bunch a"

The next day, the HR manager clarifies that while Pagliano will be officially supervised by Kennedy, he will report to managers within the bureau.

"Therefore, as you mention," she writes, "this is not a traditional supervisor/employee relationship."

Nevertheless, she continued: "This scenario does not negate Mr. Pagliano's from working in IRM."

Political appointees are not uncommon at the State Department and other government agencies. The federal Office of Personnel Management puts out a list of political appointees, known as the "Plum Book," every four years.

In the most recent State Department Plum Book, published in 2012, several hundred such positions are outlined, including about a dozen in Kennedy's department. Pagliano is listed in the Plum Book as a "Special Advisor."

A State Department official told CNN Tuesday the department does not comment on specific personnel matters.

"That said, it is standard and routine, across administrations, for the State Department's under secretary for management to be involved in the placement of Schedule C staffers within the department," the official said.

"Under Secretary Kennedy was not involved in the day-to-day supervision of Mr. Pagliano, which was left to officials in the Information Resource Management (IRM) bureau where he worked," the official added.

Pagliano's resume, which is attached to the email chains, shows he started as an IT director for the Clinton campaign in August 2006. Among his responsibilities, he lists: "Manage discrete projects as required."

He was ultimately involved in setting up Clinton's email server at her home in Chappaqua, New York, and maintained it while working at the State Department. The Clinton campaign says he was paid separately by the Clintons for all work on the server during that time.

Pagliano recently reached an immunity deal with the Justice Department to be interviewed as part of their investigation into the Clinton server.